[BioC] error installing KEGGSOAP
Steve Lianoglou
mailinglist.honeypot at gmail.com
Thu Jan 17 20:42:32 CET 2013
Hi,
Just a random question re: the KEGG stuff.
Is the suggestion that the KEGG info using KEGGREST up to date? I get
the impression that this is what's being alluded to, but I thought
that all-things-related-to-KEGG were being either (1) cutoff entirely;
or (2) restricted behind some pay wall.
Am I wrong?
-steve
On Thu, Jan 17, 2013 at 2:28 PM, Martin Morgan <mtmorgan at fhcrc.org> wrote:
> On 1/17/2013 11:11 AM, array chip wrote:
>>
>> Thanks Martin for pointing this out.
>>
>> Does this mean other KEGG packages may not be up-to-date as well if they
>> depend
>> on KEGG.db? For example, I am interested in KEGGprofile package for
>> enrichment
>> analysis. Is KEGGprofile not up-to-date now?
>
>
> I have not used KEGGprofile so do not have a direct answer; perhaps the
> maintainer will respond (packageDescription("KEGGprofile")[["Maintainer"]]).
> From a brief look, e.g., download_KEGGfile and plot_pathway, the package
> allows retrieval of data from the KEGG web site so do not necessarily use
> the KEGG.db package. On the other hand, find_enriched_pathway does seem to
> use KEGG.db.
>
> Martin
>
>>
>> Thanks
>>
>> John
>>
>>
>>
>> --------------------------------------------------------------------------------
>> *From:* Martin Morgan <mtmorgan at fhcrc.org>
>> *To:* Dan Tenenbaum <dtenenba at fhcrc.org>
>> *Cc:* array chip <arrayprofile at yahoo.com>; "bioconductor at r-project.org"
>> <bioconductor at r-project.org>
>> *Sent:* Thursday, January 17, 2013 10:53 AM
>> *Subject:* Re: [BioC] error installing KEGGSOAP
>>
>>
>> On 1/17/2013 10:45 AM, Dan Tenenbaum wrote:
>> > On Thu, Jan 17, 2013 at 10:08 AM, array chip <arrayprofile at yahoo.com
>> <mailto:arrayprofile at yahoo.com>> wrote:
>> >> Thanks Dan. For some other reason, I can't use devel version of R
>> and/or
>> >> devel Bioconductor.... Is tere any other way of getting the list of
>> genes
>> >> per KEGG pathway, and a list of available KEGG pathways?
>> >>
>> >
>> >
>> > From a web browser you can do this to get the list of all pathways:
>> > http://rest.kegg.jp/list/pathway
>> > To restrict by organism, add the kegg organism code (in this case hsa
>> > for human):
>> > http://rest.kegg.jp/list/pathway/hsa
>> >
>> > To get the genes per kegg pathway:
>> > http://rest.kegg.jp/link/genes/path:hsa00010
>> >
>> > Or just show all info about the pathway:
>> > http://rest.kegg.jp/get/path:hsa00010
>> >
>> > ...and parse out the GENE section.
>> > For both of these last two URLs you need to do a bit of parsing.
>> > KEGGREST takes care of this for you.
>>
>> Also, the KEGG.db package provides a now quite out-of-date version
>> (because of
>> changes in licensing requirements) of the KEGG data base.
>>
>> > library(org.Hs.eg.db)
>> > # discover the columns that can be queried, and the format of the
>> 'PATH' keys
>> > cols(org.Hs.eg.db)
>> [1] "ENTREZID" "PFAM" "IPI" "PROSITE" "ACCNUM"
>> [6] "ALIAS" "CHR" "CHRLOC" "CHRLOCEND" "ENZYME"
>> [11] "MAP" "PATH" "PMID" "REFSEQ" "SYMBOL"
>> [16] "UNIGENE" "ENSEMBL" "ENSEMBLPROT" "ENSEMBLTRANS"
>> "GENENAME"
>> [21] "UNIPROT" "GO" "EVIDENCE" "ONTOLOGY" "GOALL"
>> [26] "EVIDENCEALL" "ONTOLOGYALL" "OMIM" "UCSCKG"
>> > head(keys(org.Hs.eg.db, "PATH"))
>> [1] "04610" "00232" "00983" "01100" "00380" "00970"
>> > head(select(org.Hs.eg.db, "00010", "ENTREZID", "PATH"))
>> PATH ENTREZID
>> 1 00010 124
>> 2 00010 125
>> 3 00010 126
>> 4 00010 127
>> 5 00010 128
>> 6 00010 130
>> Warning message:
>> In .generateExtraRows(tab, keys, jointype) :
>> 'select' resulted in 1:many mapping between keys and return rows
>>
>> Note that on loading KEGG.db we see this:
>>
>> KEGG.db contains mappings based on older data because the original
>> resource was removed from the the public domain before the most
>> recent update was produced. This package should now be considered
>> deprecated and future versions of Bioconductor may not have it
>> available. One possible alternative to consider is to look at the
>> reactome.db package
>>
>> >
>> > Dan
>> >
>> >
>> >
>> >
>> >> Many thanks for all your help,
>> >>
>> >> John
>> >>
>> >> ________________________________
>> >> From: Dan Tenenbaum <dtenenba at fhcrc.org <mailto:dtenenba at fhcrc.org>>
>> >> To: array chip <arrayprofile at yahoo.com
>> <mailto:arrayprofile at yahoo.com>>
>> >> Cc: Martin Morgan <mtmorgan at fhcrc.org <mailto:mtmorgan at fhcrc.org>>;
>> "bioconductor at r-project.org <mailto:bioconductor at r-project.org>"
>> >> <bioconductor at r-project.org <mailto:bioconductor at r-project.org>>
>>
>> >> Sent: Thursday, January 17, 2013 9:50 AM
>> >>
>> >> Subject: Re: [BioC] error installing KEGGSOAP
>> >>
>> >> On Thu, Jan 17, 2013 at 9:45 AM, array chip <arrayprofile at yahoo.com
>> <mailto:arrayprofile at yahoo.com>> wrote:
>> >>> Thanks Dan. what package is keggLink() from?
>> >>
>> >> It's from the KEGGREST package that Martin mentioned, which is only
>> >> available in the devel version of Bioconductor (the one that will be
>> >> installed if you use R-devel (aka R 3.0)).
>> >>
>> >> Dan
>> >>
>> >>
>> >>>
>> >>> John
>> >>>
>> >>> ________________________________
>> >>> From: Dan Tenenbaum <dtenenba at fhcrc.org <mailto:dtenenba at fhcrc.org>>
>> >>> To: array chip <arrayprofile at yahoo.com
>> <mailto:arrayprofile at yahoo.com>>
>> >>> Cc: Martin Morgan <mtmorgan at fhcrc.org <mailto:mtmorgan at fhcrc.org>>;
>> "bioconductor at r-project.org <mailto:bioconductor at r-project.org>"
>> >>> <bioconductor at r-project.org <mailto:bioconductor at r-project.org>>
>>
>> >>> Sent: Thursday, January 17, 2013 7:39 AM
>> >>>
>> >>> Subject: Re: [BioC] error installing KEGGSOAP
>> >>>
>> >>> On Thu, Jan 17, 2013 at 7:14 AM, Dan Tenenbaum <dtenenba at fhcrc.org
>> <mailto:dtenenba at fhcrc.org>> wrote:
>> >>>> On Wed, Jan 16, 2013 at 11:36 PM, array chip <arrayprofile at yahoo.com
>> <mailto:arrayprofile at yahoo.com>>
>>
>> >>>> wrote:
>> >>>>> Thanks Martin. Is there a simple method to get a list of genes for
>> a
>> >>>>> given pathway?
>> >>>>>
>> >>>>
>> >>>> This is how you would do it for human:
>> >>>> keggLink("hsa", "path:hsa00010")
>> >>>>
>> >>>
>> >>> Or more generally:
>> >>> keggLink("genes", "path:hsa00010")
>> >>>
>> >>> Dan
>> >>>
>> >>>
>> >>>> Dan
>> >>>>
>> >>>>
>> >>>>> John
>> >>>>>
>> >>>>>
>> >>>>> ________________________________
>> >>>>> From: Martin Morgan <mtmorgan at fhcrc.org
>> <mailto:mtmorgan at fhcrc.org>>
>> >>>>>
>> >>>>> Cc: "bioconductor at r-project.org
>> <mailto:bioconductor at r-project.org>"
>> <bioconductor at r-project.org <mailto:bioconductor at r-project.org>>;
>> >>>>> "r-help at r-project.org <mailto:r-help at r-project.org>"
>> <r-help at r-project.org <mailto:r-help at r-project.org>>
>>
>> >>>>> Sent: Wednesday, January 16, 2013 10:38 PM
>> >>>>> Subject: Re: [BioC] error installing KEGGSOAP
>> >>>>>
>> >>>>> On 01/16/2013 05:58 PM, array chip wrote:
>> >>>>>> Hi, I am new to bioconductor, trying to install KEGGSOAP package,
>> but
>> >>>>>> got warnings() when installing and error message when trying to
>> load
>> >>>>>> the
>> >>>>>> package, can anyone suggest what went wrong?
>> >>>>>>
>> >>>>>> many thanks
>> >>>>>>
>> >>>>>> John
>> >>>>>>
>> >>>>>>
>> >>>>>>
>> >>>>>>> source("http://bioconductor.org/biocLite.R")
>> >>>>>> Bioconductor version 2.11 (BiocInstaller 1.8.3), ?biocLite for
>> help
>> >>>>>>> biocLite("KEGGSOAP")
>> >>>>>> BioC_mirror: http://bioconductor.org <http://bioconductor.org/>
>>
>> >>>>>> Using Bioconductor version 2.11 (BiocInstaller 1.8.3), R version
>> 2.15.
>> >>>>>> Installing package(s) 'KEGGSOAP'
>> >>>>>> trying URL
>> >>>>>>
>> >>>>>>
>>
>> 'http://bioconductor.org/packages/2.11/bioc/bin/windows/contrib/2.15/KEGGSOAP_1.32.0.zip'
>>
>> <http://bioconductor.org/packages/2.11/bioc/bin/windows/contrib/2.15/KEGGSOAP_1.32.0.zip%27>
>>
>> >>>>>> Content type 'application/zip' length 69037 bytes (67 Kb)
>> >>>>>> opened URL
>> >>>>>> downloaded 67 Kb
>> >>>>>>
>> >>>>>> package ‘KEGGSOAP’ successfully unpacked and MD5 sums checked
>> >>>>>>
>> >>>>>> The downloaded binary packages are in
>> >>>>>> Â Â Â Â Â Â Â
>> >>>>>> C:\Users\yzhang\AppData\Local\Temp\RtmpawAjwx\downloaded_packages
>> >>>>>> Warning message:
>> >>>>>> installed directory not writable, cannot update packages
>> 'acepack',
>> >>>>>> 'actuar', 'ada', 'ade4', 'ade4TkGUI',
>> >>>>>> Â 'agricolae', 'akima', 'ape', 'aplpack', 'arules', 'bitops',
>> 'boot',
>> >>>>>> 'Cairo', 'car', 'caTools', 'cba',
>> >>>>>> Â 'chron', 'class', 'clue', 'cluster', 'coda', 'colorspace',
>> >>>>>> 'CompQuadForm', 'corpcor', 'DAAG', 'date',
>> >>>>>> Â 'deldir', 'descr', 'deSolve', 'devtools', 'digest', 'diptest',
>> >>>>>> 'doBy', 'DoE.wrapper', 'e1071', 'effects',
>> >>>>>> Â 'ENmisc', 'epiR', 'eRm', 'evaluate', 'evd', 'FactoMineR',
>> 'fArma',
>> >>>>>> 'fAssets', 'fBasics', 'fdrtool',
>> >>>>>> Â 'fExoticOptions', 'fExtremes', 'fGarch', 'fields', 'flexclust',
>> >>>>>> 'fMultivar', 'fNonlinear', 'fOptions',
>> >>>>>> Â 'forecast', 'foreign', 'fpc', 'fracdiff', 'fRegression',
>> 'FrF2',
>> >>>>>> 'FrF2.catlg128', 'fTrading',
>> >>>>>> Â 'fUnitRoots', 'gamlss', 'gamlss.data', 'gamlss.dist', 'gclus',
>> >>>>>> 'gdata', 'geoR', 'GGally', 'ggm',
>> >>>>>> Â 'ggplot2', 'gmodels', 'gridBase', 'gWidgets', 'gWidgetstcltk',
>> 'HH',
>> >>>>>> 'Hmisc', 'httr', 'igraph',
>> >>>>>> Â 'igraph0', 'inline', 'ipred', 'isa2', 'JavaGD', 'JGR',
>> 'kernlab',
>> >>>>>> 'KernSmoot [... truncated]
>> >>>>>>
>> >>>>>>
>> >>>>>>> library(KEGGSOAP)
>> >>>>>> Loading required package: BiocGenerics
>> >>>>>>
>> >>>>>> Attaching package: ‘BiocGenerics’
>> >>>>>>
>> >>>>>> The following object(s) are masked from ‘package:stats’:
>> >>>>>>
>> >>>>>> Â Â Â xtabs
>> >>>>>>
>> >>>>>> The following object(s) are masked from ‘package:base’:
>> >>>>>>
>> >>>>>> Â Â Â anyDuplicated, cbind, colnames, duplicated, eval, Filter,
>> Find,
>> >>>>>> get, intersect, lapply, Map, mapply, mget, order, paste,
>> >>>>>> Â Â Â pmax, pmax.int, pmin, pmin.int, Position, rbind, Reduce,
>> >>>>>> rep.int,
>> >>>>>> rownames, sapply, setdiff, table, tapply, union, unique
>> >>>>>>
>> >>>>>> failed to load HTTP resource
>> >>>>>> Error : .onLoad failed in loadNamespace() for 'KEGGSOAP', details:
>> >>>>>> Â call: NULL
>> >>>>>> Â error: 1: failed to load HTTP resource
>> >>>>>>
>> >>>>>> Error: package/namespace load failed for ‘KEGGSOAP’
>> >>>>>
>> >>>>> KEGG's SOAP service has been discontinued; the package has been
>> replaced
>> >>>>> by
>> >>>>> KEGGREST, but KEGGREST is only available if using the 'devel'
>> version of
>> >>>>> R, e.g.,
>> >>>>>
>> >>>>> http://cran.fhcrc.org/bin/windows/base/rdevel.html
>> >>>>>
>> >>>>> Martin
>> >>>>>
>> >>>>>>
>> >>>>>>
>> >>>>>>> sessionInfo()
>> >>>>>> R version 2.15.1 (2012-06-22)
>> >>>>>> Platform: x86_64-pc-mingw32/x64 (64-bit)
>> >>>>>>
>> >>>>>> locale:
>> >>>>>> [1] LC_COLLATE=English_United States.1252Â
>> LC_CTYPE=English_United
>> >>>>>> States.1252Â Â
>> >>>>>> [3] LC_MONETARY=English_United States.1252 LC_NUMERIC=CÂ Â Â Â Â Â
>> Â Â
>> >>>>>> Â
>> >>>>>> Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â
>> >>>>>> [5] LC_TIME=English_United States.1252Â Â Â
>> >>>>>>
>> >>>>>> attached base packages:
>> >>>>>> [1] stats    graphics grDevices datasets utils   Â
>> >>>>>> methodsÂ
>> >>>>>>  base   Â
>> >>>>>>
>> >>>>>> other attached packages:
>> >>>>>> [1] BiocGenerics_0.4.0Â BiocInstaller_1.8.3
>> >>>>>>
>> >>>>>> loaded via a namespace (and not attached):
>> >>>>>> [1] codetools_0.2-8 RCurl_1.91-1.1Â SSOAP_0.8-0Â Â Â Â
>> tools_2.15.1Â
>> >>>>>> Â
>> >>>>>> Â XML_3.9-4.1Â Â Â Â XMLSchema_0.7-2
>> >>>>>> [[alternative HTML version deleted]]
>> >>>>>>
>> >>>>>>
>> >>>>>>
>> >>>>>> _______________________________________________
>> >>>>>> Bioconductor mailing list
>> >>>>>> Bioconductor at r-project.org <mailto:Bioconductor at r-project.org>
>>
>> >>>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>> >>>>>> Search the archives:
>> >>>>>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>> >>>>>>
>> >>>>>
>> >>>>>
>> >>>>> --
>> >>>>> Computational Biology / Fred Hutchinson Cancer Research Center
>> >>>>> 1100 Fairview Ave. N.
>> >>>>> PO Box 19024 Seattle, WA 98109
>> >>>>>
>> >>>>> Location: Arnold Building M1 B861
>> >>>>> Phone: (206) 667-2793
>> >>>>> [[alternative HTML version deleted]]
>> >>>>>
>> >>>>>
>> >>>>> _______________________________________________
>> >>>>> Bioconductor mailing list
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>>
>> >>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
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>> >>>
>> >>>
>> >>
>> >>
>>
>>
>> --
>> Dr. Martin Morgan, PhD
>> Fred Hutchinson Cancer Research Center
>> 1100 Fairview Ave. N.
>> PO Box 19024 Seattle, WA 98109
>>
>>
>
>
> --
> Dr. Martin Morgan, PhD
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N.
> PO Box 19024 Seattle, WA 98109
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
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--
Steve Lianoglou
Graduate Student: Computational Systems Biology
| Memorial Sloan-Kettering Cancer Center
| Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact
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